A series of functionalized alkanes and/or alkyl alcohols have been prepared and imaged by scanning tunneling microscopy (STM) methods on graphite surfaces. The stability of these ordered overlayers has facilitated reproducible collection of STM images at room temperature with submolecular resolution, in most cases allowing identification of individual hydrogen atoms in the alkane chains, but in all cases allowing identification of molecular length features and other aspects of the image that can be unequivocally related to the presence of functional groups in the various molecules of concern. Functional groups imaged in this study include halides (X ) F, Cl, Br, I), amines, alcohols, nitriles, alkenes, alkynes, ethers, thioethers, and disulfides. Except for -Cl and -OH, all of the other functional groups could be distinguished from each other and from -Cl or -OH through an analysis of their STM metrics and image contrast behavior. The dominance of molecular topography in producing the STM images of alkanes and alkanols was established experimentally and also was consistent with quantum chemistry calculations. Unlike the contrast of the methylene regions of the alkyl chains, the STM contrast produced by the various functional groups was not dominated by topographic effects, indicating that variations in local electronic coupling were important in producing the observed STM images of these regions of the molecules. For molecules in which electronic effects overwhelmed topographic effects in determining the image contrast, a simple model is presented to explain the variation in the electronic coupling component that produces the contrast between the various functional groups observed in the STM images. Additionally, the bias dependence of these STM images has been investigated and the contrast vs bias behavior is related to factors involving electron transfer and hole transfer that have been identified as potentially being important in dominating the electronic coupling in molecular electron transfer processes.
A theoretical model based on perturbation theory has been
developed to predict the scanning tunneling
microscopy (STM) images of molecules adsorbed on graphite. The
model is applicable to a variety of different
molecules with reasonable computational effort and provides images that
are in qualitative agreement with
experimental results. The model predicts that topographic effects
will dominate the STM images of alkanes
on graphite surfaces. The computations correlate well with the STM
data of functionalized alkanes and
allow assessment of the structure and orientation of most of the
functionalized alkanes that have been studied
experimentally. In addition, the computations suggest that the
highly diffuse virtual orbitals of the adsorbed
molecules, despite being much farther in energy from the Fermi level of
the graphite than the occupied orbitals,
may play an important role in determining the STM image contrast of
such systems.
Scanning tunneling microscopy (STM) images have been collected for a series of substituted alkanes and
alkanols that form ordered overlayers at room temperature on highly ordered pyrolytic graphite surfaces.
Molecules that have been imaged possess an internal bromide, with or without terminal alcohol groups (HO(CH2)9CHBr(CH2)10OH and H3C(CH2)16CHBr(CH2)16CH3), an internal −OH group (H3C(CH2)16CHOH(CH2)16CH3), and an internal methyl group (H3C(CH2)16CHCH3(CH2)16CH3). These data allow comparison to the
STM image contrast reported previously for molecules in which −OH, −Br, and −CH3 groups were located
in terminal positions of alkane chains adsorbed onto graphite surfaces. When the functional groups were in
gauche positions relative to the alkyl chain, and thus produced molecular features that protruded toward the
tip, the functional groups were observed to produce bright regions in a constant current STM image, regardless
of the STM contrast behavior observed for these same functional groups when they were in terminal positions
of adsorbed alkyl chains. These observations are in excellent agreement with theoretical predictions of the
STM behavior of such systems. Additionally, several interesting packing structures have been observed that
have yielded insight into the intermolecular forces that control the packing displayed by these overlayers.
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